食用菌InDel分子标记的应用现状与展望

doi:10.12190/j.issn.2096-1197.2026.04.03

Abstract

Abstract: Due to the limited number of InDel molecular markers developed in edible fungi,insufficient functional validation of candidate genes,their concentration mainly on major cultivated edible fungi,and the relatively late start of application research in edible fungi,basic research remains insufficiently in-depth. With the development of whole-genome sequencing technology,the application potential of InDel molecular markers in genetic analysis,variety identification and high-quality variety breeding of edible fungi has been further released,and the applications in the field of edible fungi research have been increasing. The paper reviews the application progress of InDel molecular markers in the evaluation of germplasm resources,variety identification and protection,and breeding of edible fungi,conducts a visual analysis of the relevant literature using VOSviewer method,and examines existing problems as well as future application directions and research priorities of this technology in the edible fungi field,with the aim of providing technical support for studies on elucidating the genetic background of strains,molecular-assisted breeding,identification of specific functional genes,and exploration of related mechanisms of edible fungi.

Key words: Edible fungi, InDel molecular markers, Genetic diversity, Molecular breeding

CLC Number:

S646

LIU Rui, LIU Yuandong, XU Yan, ZHUANG Qiuli, WANG Qi, WANG Jingwen, DANG Shuai, HAO Fengmin, YAN Lei. Current application status and prospects of InDel molecular markers in edible fungi[J].Journal of Northern Agriculture, 2026, 54(4): 24-33.

References

[1] 李玉. 中国食用菌产业发展现状、机遇和挑战:走中国特色菇业发展之路,实现食用菌产业强国之梦[J].菌物研究,2018,16(3):125-131.
[2] 中国食用菌协会.2023年度全国食用菌统计调查结果分析[J].中国食用菌,2025,44(1):120-129.
[3] Yu Qiannan,Guo Meijuan,Zhang Bin,et al.Analysis of nutritional composition in 23 kinds of edible fungi[J].Journal of Food Quality,2020,2020:8821315.
[4] 陈建胜,杨正友,王延圣,等.食用菌营养组成、功能活性及加工现状研究进展[J].食品工业科技,2024,45(12):358-366.
[5] González A,Cruz M,Losoya C,et al.Edible mushrooms as a novel protein source for functional foods[J].Food & Function,2020,11(9):7400-7414.
[6] 姜晓红,朱家漘,孙忠刚,等.基于InDel标记的杏鲍菇遗传多样性评价[J].食药用菌,2023,31(6):385-390.
[7] 付露琴. 大球盖菇种质资源遗传多样性分析及优良菌株筛选研究[D].天津:天津农学院,2025.
[8] Im C H,Park Y H,Hammel K E,et al.Construction of a genetic linkage map and analysis of quantitative trait loci associated with the agronomically important traits of Pleurotus eryngii[J].Fungal Genetics and Biology,2016, 92:50-64.
[9] 于海龙,章炉军,李洁,等.香菇不同温型菌龄菌株杂交F₁代杂种优势初步分析[J].食用菌学报,2022,29(5):22-32.
[10] 李新. 作物分子标记辅助选择育种研究进展[J].宁夏农林科技,2024,65(5):35-43.
[11] 龚文兵. 香菇重要农艺性状的QTL定位[D].武汉:华中农业大学,2014.
[12] Yang Jinchang,Meng Pengxu,Mi Hang,et al.The development of ideal insertion and deletion (InDel) markers and initial InDel map variation in cucumber using re-sequenced data[J].BMC Genomics,2025,26(1):391.
[13] Wang Tingli,Yue Shang,Jin Yating,et al.Advances allowing feasible pyrG gene editing by a CRISPR-Cas9 system for the edible mushroom Pleurotus eryngii[J].Fungal Genetics and Biology,2021,147:103509.
[14] Britten R J,Rowen L,Williams J,et al.Majority of divergence between closely related DNA samples is due to InDels[J].Proceedings of the National Academy of Sciences of the United States of America,2003,100(8):4661-4665.
[15] Santos C,Fondevila M,Ballard D,et al.Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels:results of a collaborative EDNAP exercise[J].Forensic Science International:Genetics,2015,19:56-67.
[16] Manta F,Caiafa A,Pereira R,et al.InDel markers:genetic diversity of 38 polymorphisms in Brazilian populations and application in a paternity investigation with post mortem material[J].Forensic Science International Genetics,2012,6(5):658-661.
[17] 杨洁,赫佳,王丹碧,等.InDel标记的研究和应用进展[J].生物多样性,2016,24(2):237-243.
[18] Gao Qiang,Yue Guidong,Li Wenqi,et al.Recent progress using high-throughput sequencing technologies in plant molecular breeding[J].Journal of Integrative Plant Biology,2012,54(4):215-227.
[19] Väli U,Brandström M,Johansson M,et al.Insertion-deletion polymorphisms (InDels) as genetic markers in natural populations[J].BMC Genetics,2008,9:8.
[20] Ajawatanawong P,Baldauf S L.Evolution of protein InDels in plants,animals and fungi[J].BMC Evolutionary Biology,2013,13(1):140.
[21] 杨驰,马璐,肖冬来,等.基因组测序分析广叶绣球菌SP-A菌株的遗传差异[J].菌物学报,2021,40(12):3246-3255.
[22] Gong Wenbing,Wang Yahui,Xie Chunliang,et al.Whole genome sequence of an edible and medicinal mushroom,Hericium erinaceus (Basidiomycota,Fungi)[J].Genomics,2020,112(3):2393-2399.
[23] 谭笑,滕立平,滕星,等.利用ITS-RFLP标记辅助筛选白灵侧耳与杏鲍菇杂交菌株[J].东北师大学报(自然科学版),2017,49(2):105-110.
[24] Xiang Xingjie,Li Chuang,Li Lei,et al.Genetic diversity and population structure of Chinese Lentinula edodes revealed by InDel and SSR markers[J].Mycological Progress,2016,15(4):37.
[25] Qu Jibin,Huang Chenyang,Zhang Jinxia.Genome-wide functional analysis of SSR for an edible mushroom Pleurotus ostreatus[J].Gene,2016,575(2):524-530.
[26] 赵光辉,吴汉琼,方洪枫.基于ISSR和RAPD分子标记的15株糙皮侧耳遗传多样性分析[J].热带农业科学,2023,43(12):29-33.
[27] Fu Lizhong,Zhang Hongyu,Wu Xueqian,et al.Evaluation of genetic diversity in Lentinula edodes strains using RAPD,ISSR and SRAP markers[J].World Journal of Microbiology and Biotechnology,2010,26(4):709-716.
[28] 杨和川,谭一罗,苏文英,等.基于RAPD的白色金针菇菌株遗传多样性分析[J].江西农业学报,2019,31(2):62-65.
[29] 赵光辉,方洪枫,陈剑,等.20株草菇遗传多样性的分析[J].江苏农业科学,2020,48(16):194-197.
[30] 张双双. 灰树花交配型A、B位点分子遗传学结构及SNP、InDel分析[D].保定:河北农业大学,2022.
[31] 张美彦,宋春艳,于海龙,等.基于SNP分型的香菇交配型AS-PCR鉴定[J].食用菌学报,2019,26(2):1-9.
[32] 范秀芝. 黑木耳gpd和漆酶基因克隆、表达及分子进化分析[D].武汉:华中农业大学,2013.
[33] 陈毅勇,陈国平,王松,等.DNA分子标记在食用菌研究中的应用[J].现代化农业,2017(11):33-35.
[34] 沈秀芬,章炉军,张美彦,等.利用InDel标记分析中国香菇菌株的遗传多样性与群体结构[J].菌物学报,2021,40(9):2266-2281.
[35] 张丹,庄振,季英磊,等.设施化专用香菇种质资源挖掘[J].菌物学报,2022,41(11):1889-1904.
[36] 宋琳琳,陈红芝,毋柳柳,等.基于重测序的23份香菇种质资源全基因组序列分析[J].中国瓜菜,2024,37(3):28-34.
[37] 戴建清,陈文智,曾志恒,等.双孢蘑菇As2796菌株气生与贴生菌丝遗传差异的转录组分析[J].福建农业学报,2024,39(9):1023-1034.
[38] 施肖堃,蔡志欣,郭仲杰,等.18个双孢蘑菇核心种质的重测序初步分析[J].福建农业学报,2019,34(10):1167-1172.
[39] 沈颖越,金群力,蔡为明,等.基于重测序信息的金针菇菌株资源遗传多样性及群体结构分析[J].菌物学报,2020,39(6):1016-1028.
[40] 夏会楠,李东晓,冯璠,等.平菇基因组InDel标记开发及杂交菌株遗传多样性分析[J].食用菌,2024,46(3):37-41.
[41] Cao Luping,Yang Delong,Zhang Qin,et al.Population genetic structure of Hymenopellis radicata germplasm resources based on genome re-sequencing[J].Frontiers in Microbiology,2024,15:1287641.
[42] Zeng Yukang,Shen Zhenhui,Cao Yao,et al.Genetic diversity analysis and multi-fingerprint map construction of Naematelia aurantialba germplasm resources[J].Scientific Reports,2025,15(1):44308.
[43] 沈真辉,杨林雷,曹瑶,等.基于基因组重测序开发中华包革耳(金耳菌)菌株的鉴别标记[J].菌物学报,2025,44(4):47-61.
[44] 冯璠,杨文岗,王雅暄,等.基于重测序技术对野生秀珍菇菌株鉴定及遗传差异研究[J].北方园艺,2025(9):25-34.
[45] 赵建霞. 显微观察、InDel分子标记及AbRLM基因表达分析在双孢蘑菇发育遗传研究中的应用[D].金华:浙江师范大学,2019.
[46] 范秀芝,周雁,边银丙.基于等位基因InDel快速检测黑木耳原生质体单核体[J].菌物学报,2014,33(2):273-279.
[47] Wang Gang,Lin Jingxian,Shi Yang,et al.Mitochondrial genome in Hypsizygus marmoreus and its evolution in Dikarya[J].BMC Genomics,2019,20(1):765.
[48] 卢兴潮. 毛木耳遗传连锁图构建和单核菌丝生长速度的QTL定位[D].武汉:华中农业大学,2015.
[49] Gong Wenbing,Li Lei,Zhou Yan,et al.Genetic dissection of fruiting body-related traits using quantitative trait loci mapping in Lentinula edodes[J].Applied Microbiology and Biotechnology,2016,100(12):5437-5452.
[50] 刘伟,张倩倩,舒芳,等.梯棱羊肚菌全基因组SNP/InDel分析及基于InDel标记的遗传连锁图谱构建[J].菌物学报,2019,38(12):2195-2204.
[51] Zhang Shuangshuang,Li Xiao,Li Guojie,et al.Genetic and molecular evidence of a tetrapolar mating system in the edible mushroom Grifola frondosa[J].Journal of Fungi,2023,9(10):959.
[52] 朱维佳,王蕊,薛英杰,等.兼容双平台的玉米糯质基因InDel功能标记开发与应用[J].作物学报,2025,51(9):2330-2340.
[53] 杨敏,贺涵,周陈平,等.基于重测序的番木瓜基因组InDel标记开发与应用[J].园艺学报,2025,52(10):2597-2612.
[54] Li Chuang,Gong Wenbing,Zhang Lin,et al.Association mapping reveals genetic loci associated with important agronomic traits in Lentinula edodes,shiitake mushroom[J].Frontiers in Microbiology,2017,8:237.
[55] 王湘黔,杜金茹,李林萍,等.香菇‘辽抚4号'交配型基因InDel/SNP分子标记构建及应用[J].食用菌学报,2026,33(1):1-10.
[56] 季英磊,巩梦雪,李洁,等.基于InDel标记的香菇种质资源遗传多样性分析及指纹图谱的构建[C]//中国菌物学会.中国菌物学会2023年学术年会论文摘要.上海:上海市农业科学院食用菌研究所,2023:42.
[57] 沈秀芬. 香菇菌龄性状BSA定位及InDel标记开发研究[D].长春:吉林农业大学,2021.
[58] 李巧珍,章炉军,尚晓冬,等.基于BSA技术的香菇高多糖相关的分子标记开发与验证[C]//中国食用菌协会药用真菌委员会.第十二届药用真菌学术研讨会论文集.上海:上海市农业科学院食用菌研究所,2023:111.
[59] 贾定洪,王波,何晓兰,等.基于基因组重测序发掘金针菇InDel、SV及丰度SNP标记[J].菌物学报,2024,43(7):42-53.
[60] Yamaguchi S,Sakamoto H,Tsukiyama T,et al.Development of codominant DNA markers (InDel) for enokitake mushroom Flammulina velutipes cv. “Hatsuyuki”[J].Journal of Crop Research,2023,68:61-64.
[61] 冯璠. 基于全基因组重测序的平菇遗传变异规律研究与交配型鉴定[D].邯郸:河北工程大学,2024.
[62] 夏会楠. 平菇白色变异菌株的鉴定以及单核菌株遗传规律研究[D].邯郸:河北工程大学,2023.
[63] 徐珍,陆欢,杨慧,等.基于分子辅助技术杂交选育双孢蘑菇新菌株[J].菌物学报,2025,44(10):140-151.
[64] 周超,马银鹏,包旭翔,等.DNA分子标记技术在黑木耳中的研究进展[J].北方园艺,2023(7):125-131.

Current application status and prospects of InDel molecular markers in edible fungi

PDF (PC)

Like

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Metrics

Comments

Recommended 0

[1]	LEI Xuan, ZHAO Xian, LI Juan, SHI Xuefen, DAI Yabo, YANG Guangwei, YE Jun, LU Zhanyuan. Genetic diversity analysis and comprehensive evaluation of Avena sativa germplasm resources [J]. Journal of Northern Agriculture, 2026, 54(1): 1-14.
[2]	WU Guoqiang, GAO Rui, JIN Yihang, ZHANG Guizhi, JIANG Lili, XU Jieli, JIN Guanghui. Evaluation of common scab resistance and analysis of genetic variation in traits of potato hybrid progenies [J]. Journal of Northern Agriculture, 2025, 53(5): 1-14.
[3]	YU Haibin, BAO Hongchun, LI Xiaolei, REN Yifang, ZONG Hailong, PANG Jie, YU Chuanzong, WANG Yanchun, ZHANG Wenguang. Genetic diversity analysis of 8 Morchella esculents strains based on ISSR [J]. Journal of Northern Agriculture, 2024, 52(5): 21-28.
[4]	GUO Chengyu, YI Fengyan, FANG Yongyu, SHI Zhidan, LIU Fang, ZHAO Heping, DING Haijun. Genetic diversity analysis of phenotypic traits in 99 barley germplasm resources [J]. Journal of Northern Agriculture, 2023, 51(4): 1-10.
[5]	YANG Fan, ZHANG Yanfang, WANG Jinhua, ZHAO Yuan, ZHAO Lingmin, ZHANG Xiaomeng, ZHANG Yong, HUO Xiuwen. SSR analysis of Chinese yam（Dioscorea opposita Thunb.）germplasm resources and construction of primary core collection [J]. Journal of Northern Agriculture, 2022, 50(2): 18-27.
[6]	XIAN Feng, LU Zhanyuan, ZHANG Jianzhong, CHEN Liyu, CHENG Yuchen, YANG Jianqiang, ZHANG Xiangqian, Suhe. Genetic diversity analysis of early maturing cotton germplasm resources base on SSR molecular markers [J]. Journal of Northern Agriculture, 2022, 50(1): 11-17.
[7]	HAN Zhigang, XIE Rui, JIN Xiaolei, GUO Binyu, GUO Jingshan. Genetic diversity analysis of potato germplasm resources based on phenotypic traits [J]. Journal of Northern Agriculture, 2021, 49(5): 9-17.
[8]	ZHAO Shangmin, LI Xiaodong, FU Zengjuan, E Yuanyuan, ZHANG Hui, WANG Liang, ZHANG Ziqiang, ZHENG Wenzhe, ZHANG Bizhou, BAI Chen, ZHANG Huizhong. Analysis of genetic diversity and population structure of sugarbeet germplasm resources by SSR markers [J]. Journal of Northern Agriculture, 2021, 49(1): 1-9.
[9]	CUI Guohui, YE Jun, WU Xiaohua, YANG Lei, WANG Xiaobing, TAN Liping, YU Meiling, ZHAO Chunzhi, ZHANG Chunyan, ZHANG Haibin, WU Yunxia, LI Yuanqing. Genetic diversity analysis of phenotype traits of spring wheat parental resources in Inner Mongolia [J]. Journal of Northern Agriculture, 2020, 48(3): 1-9.
[10]	CHEN Wenjin, ZHAO Cunhu, HE Xiaoyong, KONG Qingquan, ZHANG Ziqiang, CHEN Wenhe, YANG Jie. Genetic diversity analysis of agronomic characters of mung bean main cultivars [J]. Journal of Northern Agriculture, 2020, 48(3): 18-25.
[11]	PANG Peng, ZHANG Zhiyong, LI Lijun, QI Bingjie, GUO Zhanbin. Genetic diversity analysis of agronomic characters of quinoa germplasm resources [J]. Journal of Northern Agriculture, 2020, 48(3): 26-31.
[12]	YE Jun, WU Xiaohua, LI Yuanqing, CUI Guohui, WANG Xiaobin, ZHAO Chunzhi, YANG Lei, ZHANG Sanfen, ZHANG Haibin, YU Meiling. Genetic diversity analysis of phenotypic traits in quinoa germplasm resources [J]. Journal of Northern Agriculture, 2020, 48(1): 1-6.
[13]	ZHANG Rui, TANG Aijia, XIE Jihong, SHI Fengling, ZHAO Yan. DNA fingerprinting and genetic diversity analysis of Elymus pastures [J]. Journal of Northern Agriculture, 2019, 47(5): 1-8.
[14]	WANG Shanshan, ZHOU Changyan, ZHANG Xiangqian, LU Zhanyuan, YAN Jingbin, HAO Jianxi, CHENG Yuchen, ZHANG Chunyan. Yield difference analysis and genetic diversity of the main agronomic traits in aerospace breeding wheat strains [J]. Journal of Northern Agriculture, 2019, 47(3): 1-6.
[15]	CHEN Wenjin, KONG Qingquan, ZHAO Cunhu, HE Xiaoyong ,TIAN Xiaoyan, ZHANG Xiangqian, XI Xianmei （Plant Protection Institute,Inner Mongolia Academy of Agricuhural ＆ Animal Husbandry Sciences,Hohhot 010031, China）. Analysis of genetic diversity of the main agronomic traits of chickpea germplasm resources [J]. Journal of Northern Agriculture, 2018, 46(5): 9-18.